Emerging evidence suggests widespread ferruginous marine conditions promoted global seawater phosphate depletion and the maintenance of a low oxygen world at the start of the Neoproterozoic Era. However, the large-scale deposition of marine sedimentary Fe formations, as observed in the Paleoproterozoic, is rare in the early Neoproterozoic Era. We show that at the start of the Neoproterozoic, tidal flat and shallow marine environments along the northern passive margin of the West African Craton (WAC) were fully oxygenated and low in reactive Fe content, until an abrupt and prolong episode of deep-sea hydrothermal activity overwhelmed the WAC margin with strongly reducing Fe-rich hydrothermal fluids. This unique incident is recorded in meter-thick and kilometer-wide shallow marine siliciclastic platform rocks estimated to be ~883 Ma old and containing average bulk Fe content >22 wt% in the Wanimzi Formation in the Moroccan Anti-Atlas Mountains. The abrupt and conformable contact of the Fe-rich succession with the Fe-poor lower and upper transition boundaries, together with geochemical data, suggest rapid initiation and termination of seawater fertilization by the hydrothermal fluids that formed the unmetamorphosed hematite-rich ironstones. Rare Earth Element (REE) and Fe-based redox reconstruction point to an aftermath coincident with a return to shallow siliciclastic marine habitats characterized by a low reactive Fe content and negligible hydrothermal intrusion, where aerobic microbial communities flourished in well‑oxygenated waters. We propose that the early Neoproterozoic tectonic initiation of the breakup of the supercontinent Rodinia supplied large volumes of deep sea hydrothermal Fe, trace metals, and toxic metalloids like arsenic to shallow marine habitats along the WAC, resulting in rapid seawater deoxygenation.